ensembl
Sponsored Links
Sponsored Links
Secleted [ 0 ] software to compare
Results 1 - 15 of about 4
EnsEMBL::Web::Record 1.01
EnsEMBL::Web::Record is a family of modules used for managing a users persistant data in a database. more>>
EnsEMBL::Web::Record is a family of modules used for managing a users persistant data in a database.
SYNOPSIS
Many web sites now encourage users to register and login to access more advanced features, and to customise a site to their needs.
The EnsEMBL::Web::Record group of Perl modules is design to manage any arbitrary type of user created data in an SQL database. This module follows the Active Record design pattern, in that each new instantiated Record object represents a single row of a database.
That object can be manipulated programatically, and any changes made can be stored in the database with a single record->save function call.
Because arbitrary Perl data structures can be stored in this manner, EnsEMBL::Web::Record allows user preferences to be easily saved, and allows developers to implement new featurs quickly.
This module was first used (and has been abstracted from) the Ensembl genome browser (http://www.ensembl.org).
New user data can be added to the database:
use EnsEMBL::Web::Record;
my $bookmark = EnsEMBL::Web::Record->new();
$bookmark->url(http://www.ensembl.org);
$bookmark->name(Ensembl);
$bookmark->save;
...
The Record can be associated with an user id:
$record->user($id);
The same record can also be removed:
$bookmark->delete;
EnsEMBL::Web::Record also provides a number of methods for getting collections of records from the database, using a field selector.
EnsEMBL::Web::Record::find_bookmarks_by_user_id($id).
<<lessSYNOPSIS
Many web sites now encourage users to register and login to access more advanced features, and to customise a site to their needs.
The EnsEMBL::Web::Record group of Perl modules is design to manage any arbitrary type of user created data in an SQL database. This module follows the Active Record design pattern, in that each new instantiated Record object represents a single row of a database.
That object can be manipulated programatically, and any changes made can be stored in the database with a single record->save function call.
Because arbitrary Perl data structures can be stored in this manner, EnsEMBL::Web::Record allows user preferences to be easily saved, and allows developers to implement new featurs quickly.
This module was first used (and has been abstracted from) the Ensembl genome browser (http://www.ensembl.org).
New user data can be added to the database:
use EnsEMBL::Web::Record;
my $bookmark = EnsEMBL::Web::Record->new();
$bookmark->url(http://www.ensembl.org);
$bookmark->name(Ensembl);
$bookmark->save;
...
The Record can be associated with an user id:
$record->user($id);
The same record can also be removed:
$bookmark->delete;
EnsEMBL::Web::Record also provides a number of methods for getting collections of records from the database, using a field selector.
EnsEMBL::Web::Record::find_bookmarks_by_user_id($id).
Download (0.006MB)
Added: 2007-02-22 License: Perl Artistic License Price:
974 downloads
PerlPrimer 1.1.14
PerlPrimer is a free, open-source GUI application written in Perl. more>>
PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. PerlPrimer aims to automate and simplify the process of primer design.
Main features:
- Calculation of possible primer-dimers
- Retrieval of genomic or cdna sequences from Ensembl (including both sequences automatically for QPCR)
- Ability to BLAST search primers using the NCBI server or a local server
- Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.
- ORF and CpG island detection algorithms
- Ability to add cloning sequences to primers, automatically adjusted to be in-frame
- QPCR primer design without manual intron-exon boundary entry
PerlPrimer calculates primer melting temperature using J. SantaLucias extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified.
PerlPrimer is written in Perl and Perl/Tk. In addition, for QPCR functionality PerlPrimer uses the open-source Spidey executable from NCBI, and restriction enzyme data from the REBASE project is used when adding cloning sites. The program is designed to be cross-platform compatible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success using the program under Mac OS X.
Enhancements:
- Ensembl compatibility restored once again (slight change in the searchview output was causing problems)
<<lessMain features:
- Calculation of possible primer-dimers
- Retrieval of genomic or cdna sequences from Ensembl (including both sequences automatically for QPCR)
- Ability to BLAST search primers using the NCBI server or a local server
- Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.
- ORF and CpG island detection algorithms
- Ability to add cloning sequences to primers, automatically adjusted to be in-frame
- QPCR primer design without manual intron-exon boundary entry
PerlPrimer calculates primer melting temperature using J. SantaLucias extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified.
PerlPrimer is written in Perl and Perl/Tk. In addition, for QPCR functionality PerlPrimer uses the open-source Spidey executable from NCBI, and restriction enzyme data from the REBASE project is used when adding cloning sites. The program is designed to be cross-platform compatible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success using the program under Mac OS X.
Enhancements:
- Ensembl compatibility restored once again (slight change in the searchview output was causing problems)
Download (0.34MB)
Added: 2006-10-18 License: GPL (GNU General Public License) Price:
1102 downloads
Bio::Das::Lite 1.49
Bio::Das::Lite is a Perl extension for the DAS (HTTP+XML) Protocol. more>>
Bio::Das::Lite is a Perl extension for the DAS (HTTP+XML) Protocol.
SYNOPSIS
use Bio::Das::Lite;
my $bdl = Bio::Das::Lite->new_from_registry({category => Chromosome});
my $results = $bdl->features(22);
SUBROUTINES/METHODS
new : Constructor
my $das = Bio::Das::Lite->new(http://das.ensembl.org/das/ensembl1834);
my $das = Bio::Das::Lite->new({
timeout => 60,
dsn => http://user:pass@das.ensembl.org/das/ensembl1834,
http_proxy => http://user:pass@webcache.local.com:3128/,
});
Options can be: dsn (optional scalar or array ref, URLs of DAS services)
timeout (optional int, HTTP fetch timeout in seconds)
http_proxy (optional scalar, web cache or proxy if not set in %ENV)
caching (optional bool, primitive caching on/off)
callback (optional code ref, callback for processed XML blocks)
registry (optional array ref containing DAS registry service URLs
defaults to http://das.sanger.ac.uk/registry/services/das)
proxy_user (optional scalar, username for authenticating forward-proxy)
proxy_pass (optional scalar, password for authenticating forward-proxy)
user_agent (optional scalar, User-Agent HTTP request header value)
new_from_registry : Constructor
Similar to new above but supports capabilities and category
in the given hashref, using them to query the DAS registry and
configuring the DSNs accordingly.
my $das = Bio::Das::Lite->new_from_registry({
capabilities => [features],
category => [Protein Sequence],
});
Options are as above, plus
capability (optional arrayref of capabilities)
category (optional arrayref of categories)
<<lessSYNOPSIS
use Bio::Das::Lite;
my $bdl = Bio::Das::Lite->new_from_registry({category => Chromosome});
my $results = $bdl->features(22);
SUBROUTINES/METHODS
new : Constructor
my $das = Bio::Das::Lite->new(http://das.ensembl.org/das/ensembl1834);
my $das = Bio::Das::Lite->new({
timeout => 60,
dsn => http://user:pass@das.ensembl.org/das/ensembl1834,
http_proxy => http://user:pass@webcache.local.com:3128/,
});
Options can be: dsn (optional scalar or array ref, URLs of DAS services)
timeout (optional int, HTTP fetch timeout in seconds)
http_proxy (optional scalar, web cache or proxy if not set in %ENV)
caching (optional bool, primitive caching on/off)
callback (optional code ref, callback for processed XML blocks)
registry (optional array ref containing DAS registry service URLs
defaults to http://das.sanger.ac.uk/registry/services/das)
proxy_user (optional scalar, username for authenticating forward-proxy)
proxy_pass (optional scalar, password for authenticating forward-proxy)
user_agent (optional scalar, User-Agent HTTP request header value)
new_from_registry : Constructor
Similar to new above but supports capabilities and category
in the given hashref, using them to query the DAS registry and
configuring the DSNs accordingly.
my $das = Bio::Das::Lite->new_from_registry({
capabilities => [features],
category => [Protein Sequence],
});
Options are as above, plus
capability (optional arrayref of capabilities)
category (optional arrayref of categories)
Download (0.032MB)
Added: 2007-03-20 License: Perl Artistic License Price:
949 downloads
BioJava 1.30
BioJava is an open source Java components for biological computation. more>>
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.
<<less Download (9.0MB)
Added: 2005-04-01 License: LGPL (GNU Lesser General Public License) Price:
1666 downloads
Secleted [ 0 ] software to compare
- Page: 1 of 1
- 1
Copyright Notice:
Software piracy is theft, Using crack, password, serial numbers, registration codes, key generators is illegal and prevent future software development. The above ensembl search only lists software in full, demo and trial versions for free download. Download links are directly from our mirror sites or publisher sites, torrent files or links from rapidshare.com, yousendit.com or megaupload.com are not allowed
